Starting phenix.real_space_refine on Sun Sep 29 02:44:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/09_2024/7e9c_31029.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/09_2024/7e9c_31029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/09_2024/7e9c_31029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/09_2024/7e9c_31029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/09_2024/7e9c_31029.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/09_2024/7e9c_31029.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11439 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 260 5.49 5 S 3 5.16 5 C 6945 2.51 5 N 2302 2.21 5 O 2828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12338 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 770 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 710 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 781 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2652 Classifications: {'DNA': 130} Link IDs: {'rna3p': 129} Chain: "J" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2678 Classifications: {'DNA': 130} Link IDs: {'rna3p': 129} Chain: "K" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1204 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain breaks: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'AYA:plan-2': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 7.63, per 1000 atoms: 0.62 Number of scatterers: 12338 At special positions: 0 Unit cell: (116, 117, 111, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 P 260 15.00 O 2828 8.00 N 2302 7.00 C 6945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 61.6% alpha, 6.1% beta 116 base pairs and 176 stacking pairs defined. Time for finding SS restraints: 5.11 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.976A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.513A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 53 through 76 removed outlier: 3.656A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.661A pdb=" N ALA C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.176A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.522A pdb=" N LYS C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 4.037A pdb=" N THR D 51 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 87 removed outlier: 3.673A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 105 Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.964A pdb=" N LYS D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 55 removed outlier: 4.130A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.879A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.506A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.563A pdb=" N ILE E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.086A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.420A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.917A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.383A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.552A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 98 removed outlier: 3.898A pdb=" N LEU G 97 " --> pdb=" O GLU G 93 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 93 through 98' Processing helix chain 'H' and resid 40 through 52 removed outlier: 3.881A pdb=" N THR H 51 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 87 removed outlier: 3.608A pdb=" N ASN H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 107 through 125 removed outlier: 3.810A pdb=" N LYS H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 199 removed outlier: 4.219A pdb=" N ALA K 194 " --> pdb=" O GLU K 190 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 212 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.332A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 4.112A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.251A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.853A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.463A pdb=" N ARG G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'K' and resid 14 through 16 removed outlier: 4.257A pdb=" N LEU K 41 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 138 through 141 removed outlier: 4.187A pdb=" N LEU K 85 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU K 74 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP K 86 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL K 57 " --> pdb=" O ARG K 148 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG K 148 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS K 59 " --> pdb=" O PHE K 146 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE K 146 " --> pdb=" O HIS K 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 131 through 134 removed outlier: 7.524A pdb=" N LEU K 132 " --> pdb=" O ARG K 174 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE K 176 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU K 134 " --> pdb=" O ILE K 176 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N MET K 153 " --> pdb=" O VAL K 173 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N TYR K 175 " --> pdb=" O MET K 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 389 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 301 hydrogen bonds 598 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 176 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2508 1.33 - 1.45: 4019 1.45 - 1.57: 6024 1.57 - 1.69: 518 1.69 - 1.81: 5 Bond restraints: 13074 Sorted by residual: bond pdb=" N AYA K 2 " pdb=" CT AYA K 2 " ideal model delta sigma weight residual 1.340 1.387 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" N AYA K 2 " pdb=" CA AYA K 2 " ideal model delta sigma weight residual 1.458 1.437 0.021 1.90e-02 2.77e+03 1.23e+00 bond pdb=" CA ILE C 80 " pdb=" CB ILE C 80 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 9.91e-01 bond pdb=" CT AYA K 2 " pdb=" OT AYA K 2 " ideal model delta sigma weight residual 1.226 1.246 -0.020 2.00e-02 2.50e+03 9.76e-01 ... (remaining 13069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 18314 1.64 - 3.29: 411 3.29 - 4.93: 45 4.93 - 6.57: 12 6.57 - 8.22: 2 Bond angle restraints: 18784 Sorted by residual: angle pdb=" C ALA K 204 " pdb=" N GLN K 205 " pdb=" CA GLN K 205 " ideal model delta sigma weight residual 120.31 114.85 5.46 1.52e+00 4.33e-01 1.29e+01 angle pdb=" CB ARG A 52 " pdb=" CG ARG A 52 " pdb=" CD ARG A 52 " ideal model delta sigma weight residual 111.30 119.52 -8.22 2.30e+00 1.89e-01 1.28e+01 angle pdb=" N GLN K 205 " pdb=" CA GLN K 205 " pdb=" CB GLN K 205 " ideal model delta sigma weight residual 110.28 115.34 -5.06 1.55e+00 4.16e-01 1.06e+01 angle pdb=" CB ARG A 53 " pdb=" CG ARG A 53 " pdb=" CD ARG A 53 " ideal model delta sigma weight residual 111.30 118.79 -7.49 2.30e+00 1.89e-01 1.06e+01 angle pdb=" N GLU K 206 " pdb=" CA GLU K 206 " pdb=" CB GLU K 206 " ideal model delta sigma weight residual 110.12 114.67 -4.55 1.47e+00 4.63e-01 9.56e+00 ... (remaining 18779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.14: 5644 29.14 - 58.29: 1366 58.29 - 87.43: 144 87.43 - 116.57: 3 116.57 - 145.72: 2 Dihedral angle restraints: 7159 sinusoidal: 4551 harmonic: 2608 Sorted by residual: dihedral pdb=" C4' DC I 24 " pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " pdb=" P DG I 25 " ideal model delta sinusoidal sigma weight residual 220.00 74.28 145.72 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" C4' DG I 63 " pdb=" C3' DG I 63 " pdb=" O3' DG I 63 " pdb=" P DC I 64 " ideal model delta sinusoidal sigma weight residual 220.00 75.24 144.76 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 7156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1878 0.047 - 0.094: 223 0.094 - 0.141: 59 0.141 - 0.189: 3 0.189 - 0.236: 1 Chirality restraints: 2164 Sorted by residual: chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CG LEU A 48 " pdb=" CB LEU A 48 " pdb=" CD1 LEU A 48 " pdb=" CD2 LEU A 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA GLN K 205 " pdb=" N GLN K 205 " pdb=" C GLN K 205 " pdb=" CB GLN K 205 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 2161 not shown) Planarity restraints: 1475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 136 " -0.005 2.00e-02 2.50e+03 1.17e-02 4.10e+00 pdb=" N9 DG J 136 " 0.004 2.00e-02 2.50e+03 pdb=" C8 DG J 136 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 136 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG J 136 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG J 136 " 0.029 2.00e-02 2.50e+03 pdb=" O6 DG J 136 " -0.026 2.00e-02 2.50e+03 pdb=" N1 DG J 136 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG J 136 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG J 136 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG J 136 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG J 136 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO B 32 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 105 " -0.020 2.00e-02 2.50e+03 1.03e-02 2.63e+00 pdb=" N1 DT I 105 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT I 105 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 105 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DT I 105 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 105 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 105 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 105 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 105 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 105 " 0.000 2.00e-02 2.50e+03 ... (remaining 1472 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1614 2.76 - 3.29: 11701 3.29 - 3.83: 23832 3.83 - 4.36: 25834 4.36 - 4.90: 38608 Nonbonded interactions: 101589 Sorted by model distance: nonbonded pdb=" OD1 ASN K 21 " pdb=" OH TYR K 40 " model vdw 2.221 3.040 nonbonded pdb=" O ILE E 62 " pdb=" NE2 GLN E 93 " model vdw 2.225 3.120 nonbonded pdb=" OG1 THR K 78 " pdb=" O ASN K 81 " model vdw 2.232 3.040 nonbonded pdb=" N4 DC I 64 " pdb=" N6 DA I 65 " model vdw 2.236 3.200 nonbonded pdb=" O ILE A 119 " pdb=" OG SER B 47 " model vdw 2.280 3.040 ... (remaining 101584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 132)) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 116)) selection = (chain 'G' and (resid 16 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 116)) } ncs_group { reference = (chain 'D' and (resid 35 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 127)) selection = (chain 'H' and (resid 35 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 127)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.750 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13074 Z= 0.164 Angle : 0.583 8.215 18784 Z= 0.349 Chirality : 0.035 0.236 2164 Planarity : 0.003 0.043 1475 Dihedral : 26.936 145.718 5471 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.28), residues: 875 helix: 1.26 (0.23), residues: 518 sheet: -0.56 (0.99), residues: 29 loop : -1.76 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 86 HIS 0.007 0.001 HIS G 113 PHE 0.025 0.001 PHE H 73 TYR 0.016 0.001 TYR D 45 ARG 0.019 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.7910 (pm20) cc_final: 0.7513 (pm20) REVERT: B 83 SER cc_start: 0.8215 (t) cc_final: 0.7960 (t) REVERT: B 98 TYR cc_start: 0.7617 (m-10) cc_final: 0.7384 (m-10) REVERT: C 34 LEU cc_start: 0.8841 (tp) cc_final: 0.8631 (tp) REVERT: C 82 ARG cc_start: 0.8508 (tpt90) cc_final: 0.7864 (tpt90) REVERT: D 46 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8013 (mtpt) REVERT: D 71 ASP cc_start: 0.8258 (t70) cc_final: 0.7830 (t0) REVERT: E 130 LEU cc_start: 0.8284 (tp) cc_final: 0.7943 (tp) REVERT: F 52 GLU cc_start: 0.7666 (tp30) cc_final: 0.7423 (mm-30) REVERT: G 37 ARG cc_start: 0.7496 (mmp80) cc_final: 0.6440 (mtm-85) REVERT: G 57 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7529 (tm-30) REVERT: G 65 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7389 (tm-30) REVERT: H 71 ASP cc_start: 0.7979 (t70) cc_final: 0.7486 (t0) REVERT: H 79 GLU cc_start: 0.8357 (tp30) cc_final: 0.7946 (tp30) REVERT: H 111 LYS cc_start: 0.8181 (tmmt) cc_final: 0.7913 (tmtt) REVERT: K 13 ILE cc_start: 0.4961 (mt) cc_final: 0.4726 (pt) REVERT: K 52 ARG cc_start: 0.7312 (ttp-170) cc_final: 0.6795 (ttp-170) REVERT: K 75 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.6642 (mtm180) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2843 time to fit residues: 77.1990 Evaluate side-chains 160 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 93 GLN D 98 GLN E 55 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 115 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13074 Z= 0.257 Angle : 0.601 7.355 18784 Z= 0.347 Chirality : 0.037 0.167 2164 Planarity : 0.005 0.063 1475 Dihedral : 30.621 149.344 3811 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.46 % Allowed : 15.21 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.28), residues: 875 helix: 1.18 (0.23), residues: 526 sheet: -0.70 (0.89), residues: 33 loop : -1.64 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 11 HIS 0.008 0.001 HIS F 75 PHE 0.011 0.002 PHE A 54 TYR 0.022 0.002 TYR D 45 ARG 0.008 0.001 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8374 (tm-30) REVERT: B 27 GLN cc_start: 0.8183 (pm20) cc_final: 0.7744 (pm20) REVERT: B 52 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8166 (tm-30) REVERT: B 100 PHE cc_start: 0.8265 (m-10) cc_final: 0.7986 (m-10) REVERT: C 34 LEU cc_start: 0.9028 (tp) cc_final: 0.8668 (tp) REVERT: C 57 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7817 (tm-30) REVERT: C 82 ARG cc_start: 0.8613 (tpt90) cc_final: 0.7952 (tpt90) REVERT: C 90 ASN cc_start: 0.9248 (m-40) cc_final: 0.8823 (m-40) REVERT: C 93 GLU cc_start: 0.7832 (pm20) cc_final: 0.7456 (pm20) REVERT: D 46 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8635 (mtmt) REVERT: D 71 ASP cc_start: 0.8338 (t70) cc_final: 0.7793 (t0) REVERT: F 52 GLU cc_start: 0.7798 (tp30) cc_final: 0.7329 (tp30) REVERT: G 37 ARG cc_start: 0.7602 (mmp80) cc_final: 0.6604 (mtm-85) REVERT: G 57 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7659 (tm-30) REVERT: G 65 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7220 (tm-30) REVERT: H 79 GLU cc_start: 0.8402 (tp30) cc_final: 0.8023 (tp30) REVERT: K 52 ARG cc_start: 0.7383 (ttp-170) cc_final: 0.6822 (ttp-170) REVERT: K 54 ASP cc_start: 0.7094 (m-30) cc_final: 0.6763 (p0) REVERT: K 75 ARG cc_start: 0.7284 (ttp-170) cc_final: 0.6919 (ttm170) outliers start: 25 outliers final: 19 residues processed: 212 average time/residue: 0.3026 time to fit residues: 85.5877 Evaluate side-chains 181 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 13074 Z= 0.447 Angle : 0.753 11.142 18784 Z= 0.427 Chirality : 0.043 0.203 2164 Planarity : 0.007 0.090 1475 Dihedral : 31.655 152.630 3811 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 7.88 % Allowed : 18.40 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.27), residues: 875 helix: 0.54 (0.22), residues: 527 sheet: -0.91 (0.96), residues: 29 loop : -2.13 (0.30), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 11 HIS 0.011 0.002 HIS F 75 PHE 0.025 0.003 PHE F 100 TYR 0.037 0.003 TYR D 43 ARG 0.009 0.001 ARG K 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 229 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8250 (tm-30) REVERT: A 81 ASP cc_start: 0.8324 (m-30) cc_final: 0.8098 (m-30) REVERT: A 86 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7680 (m) REVERT: B 27 GLN cc_start: 0.8404 (pm20) cc_final: 0.8095 (pm20) REVERT: B 39 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8019 (mmt-90) REVERT: C 82 ARG cc_start: 0.8803 (tpt90) cc_final: 0.7974 (tpt90) REVERT: D 95 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.6812 (ttm170) REVERT: D 116 GLU cc_start: 0.8208 (tp30) cc_final: 0.7361 (tm-30) REVERT: E 80 THR cc_start: 0.8349 (m) cc_final: 0.7715 (p) REVERT: F 52 GLU cc_start: 0.8271 (tp30) cc_final: 0.7926 (tp30) REVERT: F 74 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8684 (mm-30) REVERT: G 37 ARG cc_start: 0.8238 (mmp80) cc_final: 0.8009 (mmt90) REVERT: G 40 TYR cc_start: 0.8385 (m-10) cc_final: 0.8037 (m-80) REVERT: G 57 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7584 (tm-30) REVERT: G 65 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7699 (tm-30) REVERT: G 91 ASP cc_start: 0.7220 (t0) cc_final: 0.6809 (t0) REVERT: H 36 ARG cc_start: 0.7834 (mmm160) cc_final: 0.7370 (mmm160) REVERT: H 46 LYS cc_start: 0.8924 (mttp) cc_final: 0.8668 (mttp) REVERT: H 122 THR cc_start: 0.9183 (m) cc_final: 0.8856 (p) REVERT: K 52 ARG cc_start: 0.7527 (ttp-170) cc_final: 0.7110 (ttp-170) REVERT: K 206 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7283 (mp0) outliers start: 57 outliers final: 37 residues processed: 259 average time/residue: 0.3071 time to fit residues: 105.1121 Evaluate side-chains 239 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 40.0000 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN E 93 GLN F 25 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13074 Z= 0.235 Angle : 0.611 7.149 18784 Z= 0.356 Chirality : 0.037 0.170 2164 Planarity : 0.005 0.065 1475 Dihedral : 31.356 148.590 3811 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 6.36 % Allowed : 24.90 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 875 helix: 0.99 (0.22), residues: 532 sheet: -0.74 (0.94), residues: 29 loop : -2.02 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 11 HIS 0.007 0.001 HIS B 75 PHE 0.015 0.002 PHE F 100 TYR 0.028 0.002 TYR B 88 ARG 0.007 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 225 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8187 (tm-30) REVERT: B 27 GLN cc_start: 0.8446 (pm20) cc_final: 0.8061 (pm20) REVERT: B 44 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8518 (mmmm) REVERT: B 77 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8730 (mmtm) REVERT: C 82 ARG cc_start: 0.8739 (tpt90) cc_final: 0.8010 (tpt90) REVERT: C 91 ASP cc_start: 0.8196 (t0) cc_final: 0.7475 (t0) REVERT: D 116 GLU cc_start: 0.8198 (tp30) cc_final: 0.7271 (tm-30) REVERT: E 52 ARG cc_start: 0.9191 (mtm-85) cc_final: 0.8990 (ptp90) REVERT: E 95 SER cc_start: 0.8721 (t) cc_final: 0.8094 (p) REVERT: F 52 GLU cc_start: 0.7883 (tp30) cc_final: 0.7424 (tp30) REVERT: G 57 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7338 (tm-30) REVERT: G 65 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7438 (tm-30) REVERT: G 91 ASP cc_start: 0.7222 (t0) cc_final: 0.6743 (t0) REVERT: H 46 LYS cc_start: 0.8848 (mttp) cc_final: 0.8606 (mttp) REVERT: H 122 THR cc_start: 0.9186 (m) cc_final: 0.8915 (p) REVERT: K 52 ARG cc_start: 0.7463 (ttp-170) cc_final: 0.7036 (ttp-170) REVERT: K 86 TRP cc_start: 0.6550 (m-90) cc_final: 0.6141 (m-90) outliers start: 46 outliers final: 32 residues processed: 246 average time/residue: 0.2925 time to fit residues: 96.7857 Evaluate side-chains 244 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13074 Z= 0.263 Angle : 0.623 7.925 18784 Z= 0.359 Chirality : 0.037 0.163 2164 Planarity : 0.005 0.069 1475 Dihedral : 31.217 146.762 3811 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 7.47 % Allowed : 25.86 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 875 helix: 1.13 (0.22), residues: 539 sheet: -0.63 (0.93), residues: 29 loop : -2.05 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 11 HIS 0.011 0.001 HIS F 75 PHE 0.023 0.002 PHE F 100 TYR 0.028 0.002 TYR B 88 ARG 0.010 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 220 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8336 (tm-30) REVERT: B 27 GLN cc_start: 0.8461 (pm20) cc_final: 0.8089 (pm20) REVERT: B 39 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8101 (mmt-90) REVERT: B 44 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8724 (mmmm) REVERT: B 77 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8849 (mmtt) REVERT: C 33 ARG cc_start: 0.8386 (ptm-80) cc_final: 0.8121 (ptm-80) REVERT: C 40 TYR cc_start: 0.7513 (m-80) cc_final: 0.7024 (m-80) REVERT: C 82 ARG cc_start: 0.8759 (tpt90) cc_final: 0.7962 (tpt90) REVERT: C 91 ASP cc_start: 0.8257 (t0) cc_final: 0.7628 (t0) REVERT: D 116 GLU cc_start: 0.8169 (tp30) cc_final: 0.7271 (tm-30) REVERT: E 95 SER cc_start: 0.8612 (t) cc_final: 0.8073 (p) REVERT: F 52 GLU cc_start: 0.7816 (tp30) cc_final: 0.7474 (tm-30) REVERT: F 74 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8664 (mm-30) REVERT: G 57 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7323 (tm-30) REVERT: G 65 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7433 (tm-30) REVERT: G 91 ASP cc_start: 0.7256 (t0) cc_final: 0.6947 (t0) REVERT: H 46 LYS cc_start: 0.8878 (mttp) cc_final: 0.8642 (mttp) REVERT: H 122 THR cc_start: 0.9191 (m) cc_final: 0.8921 (p) REVERT: K 52 ARG cc_start: 0.7420 (ttp-170) cc_final: 0.6867 (ttp-170) REVERT: K 206 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7246 (mp0) outliers start: 54 outliers final: 41 residues processed: 246 average time/residue: 0.2996 time to fit residues: 97.9924 Evaluate side-chains 236 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 193 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 40 TYR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 105 optimal weight: 30.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13074 Z= 0.278 Angle : 0.633 8.006 18784 Z= 0.364 Chirality : 0.038 0.171 2164 Planarity : 0.005 0.075 1475 Dihedral : 31.248 147.322 3811 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 7.75 % Allowed : 26.83 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.27), residues: 875 helix: 1.21 (0.22), residues: 533 sheet: -0.20 (0.96), residues: 29 loop : -2.11 (0.30), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 11 HIS 0.007 0.001 HIS B 75 PHE 0.014 0.002 PHE A 54 TYR 0.018 0.002 TYR B 88 ARG 0.010 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 213 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 52 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.7854 (mtm180) REVERT: A 129 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7580 (tpt90) REVERT: B 27 GLN cc_start: 0.8430 (pm20) cc_final: 0.8079 (pm20) REVERT: B 39 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8209 (mmt-90) REVERT: B 74 GLU cc_start: 0.8717 (tt0) cc_final: 0.8489 (mm-30) REVERT: B 77 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8621 (mmtm) REVERT: C 40 TYR cc_start: 0.7648 (m-80) cc_final: 0.7276 (m-80) REVERT: C 62 GLU cc_start: 0.8188 (tp30) cc_final: 0.7974 (tt0) REVERT: C 82 ARG cc_start: 0.8797 (tpt90) cc_final: 0.7963 (tpt90) REVERT: C 91 ASP cc_start: 0.8269 (t0) cc_final: 0.7582 (t0) REVERT: D 116 GLU cc_start: 0.8161 (tp30) cc_final: 0.7189 (tm-30) REVERT: E 97 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: F 23 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7682 (mmm160) REVERT: F 52 GLU cc_start: 0.7838 (tp30) cc_final: 0.7503 (tm-30) REVERT: F 74 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8749 (mm-30) REVERT: G 40 TYR cc_start: 0.8038 (m-80) cc_final: 0.7673 (m-80) REVERT: G 57 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7319 (tm-30) REVERT: G 65 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7451 (tm-30) REVERT: G 91 ASP cc_start: 0.7277 (t0) cc_final: 0.6922 (t0) REVERT: H 46 LYS cc_start: 0.8888 (mttp) cc_final: 0.8666 (mttp) REVERT: K 52 ARG cc_start: 0.7377 (ttp-170) cc_final: 0.6861 (ttp-170) REVERT: K 206 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7264 (mp0) outliers start: 56 outliers final: 44 residues processed: 237 average time/residue: 0.3019 time to fit residues: 95.3087 Evaluate side-chains 246 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 198 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 50.0000 chunk 68 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS D 66 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13074 Z= 0.181 Angle : 0.610 12.335 18784 Z= 0.349 Chirality : 0.036 0.163 2164 Planarity : 0.004 0.048 1475 Dihedral : 30.923 147.043 3811 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.81 % Allowed : 28.49 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.28), residues: 875 helix: 1.48 (0.23), residues: 543 sheet: -0.32 (0.88), residues: 35 loop : -2.15 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 11 HIS 0.005 0.001 HIS F 75 PHE 0.016 0.002 PHE F 100 TYR 0.015 0.002 TYR K 40 ARG 0.010 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 226 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 52 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.7818 (mtm180) REVERT: A 63 ARG cc_start: 0.7519 (mmm160) cc_final: 0.7010 (tpm170) REVERT: A 76 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: A 129 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7638 (tpt90) REVERT: B 27 GLN cc_start: 0.8434 (pm20) cc_final: 0.8018 (pm20) REVERT: B 39 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8107 (mmt-90) REVERT: B 77 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8459 (mmtm) REVERT: C 33 ARG cc_start: 0.8205 (ptm-80) cc_final: 0.7770 (ptm-80) REVERT: C 82 ARG cc_start: 0.8684 (tpt90) cc_final: 0.7954 (tpt90) REVERT: C 91 ASP cc_start: 0.8107 (t0) cc_final: 0.7758 (t70) REVERT: E 52 ARG cc_start: 0.9124 (ptp90) cc_final: 0.8906 (mtm-85) REVERT: E 55 GLN cc_start: 0.9116 (mt0) cc_final: 0.8778 (mt0) REVERT: E 61 LEU cc_start: 0.8080 (mt) cc_final: 0.7821 (mp) REVERT: E 95 SER cc_start: 0.8613 (t) cc_final: 0.7969 (p) REVERT: F 52 GLU cc_start: 0.7378 (tp30) cc_final: 0.6859 (tp30) REVERT: G 33 ARG cc_start: 0.7530 (tmm-80) cc_final: 0.7242 (tmm-80) REVERT: G 40 TYR cc_start: 0.8020 (m-80) cc_final: 0.7812 (m-80) REVERT: G 57 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7513 (tm-30) REVERT: G 65 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7409 (tm-30) REVERT: G 91 ASP cc_start: 0.7353 (t0) cc_final: 0.7024 (t0) REVERT: G 93 GLU cc_start: 0.6533 (pm20) cc_final: 0.6250 (pm20) REVERT: K 52 ARG cc_start: 0.7270 (ttp-170) cc_final: 0.6768 (ttp-170) REVERT: K 206 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7283 (mp0) outliers start: 42 outliers final: 28 residues processed: 246 average time/residue: 0.3061 time to fit residues: 99.9152 Evaluate side-chains 235 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 203 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 40.0000 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13074 Z= 0.212 Angle : 0.608 8.539 18784 Z= 0.348 Chirality : 0.036 0.152 2164 Planarity : 0.005 0.048 1475 Dihedral : 30.893 147.009 3811 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.67 % Allowed : 29.60 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.28), residues: 875 helix: 1.41 (0.22), residues: 547 sheet: -0.44 (0.87), residues: 35 loop : -2.03 (0.32), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 86 HIS 0.014 0.001 HIS F 75 PHE 0.008 0.001 PHE A 54 TYR 0.025 0.002 TYR H 86 ARG 0.010 0.001 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 129 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7657 (tpt90) REVERT: B 27 GLN cc_start: 0.8387 (pm20) cc_final: 0.8012 (pm20) REVERT: B 39 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8101 (mmt-90) REVERT: B 77 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8508 (mmtm) REVERT: C 33 ARG cc_start: 0.8304 (ptm-80) cc_final: 0.7795 (ptm-80) REVERT: C 40 TYR cc_start: 0.7395 (m-80) cc_final: 0.7107 (m-80) REVERT: C 82 ARG cc_start: 0.8715 (tpt90) cc_final: 0.7950 (tpt90) REVERT: C 91 ASP cc_start: 0.8146 (t0) cc_final: 0.7730 (t0) REVERT: D 116 GLU cc_start: 0.8270 (tp30) cc_final: 0.7155 (tm-30) REVERT: E 52 ARG cc_start: 0.9154 (ptp90) cc_final: 0.8868 (mtm-85) REVERT: E 55 GLN cc_start: 0.9080 (mt0) cc_final: 0.8722 (mt0) REVERT: E 128 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7856 (mmm-85) REVERT: F 52 GLU cc_start: 0.7510 (tp30) cc_final: 0.6954 (tp30) REVERT: F 74 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8601 (mm-30) REVERT: G 33 ARG cc_start: 0.7494 (tmm-80) cc_final: 0.7213 (tmm-80) REVERT: G 40 TYR cc_start: 0.7964 (m-80) cc_final: 0.7738 (m-80) REVERT: G 57 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7356 (tm-30) REVERT: G 65 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7428 (tm-30) REVERT: G 91 ASP cc_start: 0.7328 (t0) cc_final: 0.7112 (t0) REVERT: K 52 ARG cc_start: 0.7323 (ttp-170) cc_final: 0.6799 (ttp-170) REVERT: K 92 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6794 (mtt180) REVERT: K 189 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8409 (mp) REVERT: K 206 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7325 (mp0) outliers start: 41 outliers final: 32 residues processed: 226 average time/residue: 0.2792 time to fit residues: 85.5543 Evaluate side-chains 236 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 200 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 40.0000 chunk 65 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN E 93 GLN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13074 Z= 0.301 Angle : 0.660 7.956 18784 Z= 0.374 Chirality : 0.039 0.179 2164 Planarity : 0.005 0.071 1475 Dihedral : 31.189 148.056 3811 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.67 % Allowed : 30.57 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.28), residues: 875 helix: 1.21 (0.22), residues: 540 sheet: -0.51 (0.85), residues: 35 loop : -2.00 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 86 HIS 0.014 0.002 HIS F 75 PHE 0.012 0.002 PHE F 100 TYR 0.022 0.002 TYR H 86 ARG 0.009 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8186 (tm-30) REVERT: A 129 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7558 (tpt90) REVERT: B 27 GLN cc_start: 0.8389 (pm20) cc_final: 0.8150 (pm20) REVERT: B 39 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8246 (mmt-90) REVERT: B 77 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8738 (mmtt) REVERT: C 33 ARG cc_start: 0.8381 (ptm-80) cc_final: 0.7971 (ptm-80) REVERT: C 37 ARG cc_start: 0.7585 (mmp80) cc_final: 0.7327 (mmt180) REVERT: C 40 TYR cc_start: 0.7677 (m-80) cc_final: 0.7328 (m-80) REVERT: C 82 ARG cc_start: 0.8839 (tpt90) cc_final: 0.7989 (tpt90) REVERT: C 91 ASP cc_start: 0.8389 (t0) cc_final: 0.7745 (t0) REVERT: D 116 GLU cc_start: 0.8327 (tp30) cc_final: 0.7229 (tm-30) REVERT: E 52 ARG cc_start: 0.9107 (ptp90) cc_final: 0.8816 (mtm-85) REVERT: F 52 GLU cc_start: 0.7915 (tp30) cc_final: 0.7618 (tm-30) REVERT: G 33 ARG cc_start: 0.7649 (tmm-80) cc_final: 0.7028 (tmm-80) REVERT: G 57 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7356 (tm-30) REVERT: G 65 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7525 (tm-30) REVERT: G 91 ASP cc_start: 0.7256 (t0) cc_final: 0.7026 (t0) REVERT: K 206 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7283 (mp0) outliers start: 41 outliers final: 34 residues processed: 224 average time/residue: 0.2893 time to fit residues: 87.3171 Evaluate side-chains 233 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN D 66 ASN E 93 GLN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13074 Z= 0.325 Angle : 0.679 11.644 18784 Z= 0.384 Chirality : 0.039 0.264 2164 Planarity : 0.005 0.070 1475 Dihedral : 31.246 149.016 3811 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.81 % Allowed : 30.15 % Favored : 64.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.27), residues: 875 helix: 1.07 (0.22), residues: 540 sheet: -0.32 (0.89), residues: 35 loop : -2.02 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 86 HIS 0.014 0.002 HIS F 75 PHE 0.018 0.002 PHE D 68 TYR 0.024 0.002 TYR H 86 ARG 0.009 0.001 ARG E 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 52 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.8098 (mtt90) REVERT: A 76 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: A 129 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7539 (tpt90) REVERT: B 27 GLN cc_start: 0.8354 (pm20) cc_final: 0.8121 (pm20) REVERT: B 39 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8275 (mmt-90) REVERT: B 77 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8725 (mmtt) REVERT: C 33 ARG cc_start: 0.8408 (ptm-80) cc_final: 0.8013 (ptm-80) REVERT: C 37 ARG cc_start: 0.7612 (mmp80) cc_final: 0.7353 (mmt180) REVERT: C 40 TYR cc_start: 0.7775 (m-80) cc_final: 0.7476 (m-80) REVERT: C 82 ARG cc_start: 0.8873 (tpt90) cc_final: 0.7900 (tpt90) REVERT: C 91 ASP cc_start: 0.8296 (t0) cc_final: 0.7606 (t0) REVERT: D 116 GLU cc_start: 0.8290 (tp30) cc_final: 0.7200 (tm-30) REVERT: E 52 ARG cc_start: 0.9123 (ptp90) cc_final: 0.8823 (mtm-85) REVERT: E 128 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.8011 (mmm-85) REVERT: F 52 GLU cc_start: 0.7903 (tp30) cc_final: 0.7603 (tm-30) REVERT: G 40 TYR cc_start: 0.7982 (m-80) cc_final: 0.7691 (m-80) REVERT: G 42 GLN cc_start: 0.8944 (mt0) cc_final: 0.8596 (mp10) REVERT: G 57 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7637 (tm-30) REVERT: G 65 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7637 (tm-30) REVERT: G 91 ASP cc_start: 0.7247 (t0) cc_final: 0.6940 (t0) REVERT: K 43 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6739 (mtt-85) REVERT: K 52 ARG cc_start: 0.7202 (ttp-170) cc_final: 0.6694 (ttp-170) REVERT: K 206 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7349 (mp0) outliers start: 42 outliers final: 33 residues processed: 228 average time/residue: 0.2933 time to fit residues: 90.5360 Evaluate side-chains 233 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.114946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.076578 restraints weight = 35065.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078959 restraints weight = 18101.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.080447 restraints weight = 12641.937| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13074 Z= 0.215 Angle : 0.651 11.547 18784 Z= 0.367 Chirality : 0.038 0.193 2164 Planarity : 0.005 0.066 1475 Dihedral : 31.149 149.086 3811 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.84 % Allowed : 31.95 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.28), residues: 875 helix: 1.22 (0.22), residues: 549 sheet: -0.08 (0.89), residues: 35 loop : -2.18 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 86 HIS 0.013 0.001 HIS F 75 PHE 0.014 0.002 PHE B 100 TYR 0.020 0.002 TYR H 86 ARG 0.008 0.001 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2464.55 seconds wall clock time: 44 minutes 42.98 seconds (2682.98 seconds total)